[Biococoa-dev] New Structure for BioCocoa
Alexander Griekspoor
mek at mekentosj.com
Mon Jul 4 04:50:46 EDT 2005
About the IO discussion.
If we want a separate IO framework(s), I would suggest to keep all IO
in one framework, the examples you give are all sequence related, so
would depend only on the core framework (BCFoundation) right. If say
the HMM framework would need some kind of special structure, than we
can always opt to either define the structure in the foundation, but
put all other stuff in the HMM framework, or place the HMM specific
IO in the HMM framework as it is probably consists of only a few
methods anyway.
But my main question is whether we really want to separate the IO
framework as being independent. BCFoundation is so much related with
IO that I don't really see a need to separate them. Most important, I
don't think the IO will be so much code that it will be a large
framework, or that it will make the foundation so bloated. It's two
files right now! So why don't we make BCFoundation contain the IO
like it does now. And the HMM framework contains its IO etc.
IMHO a basic core that defines sequences and can IO them doesn't have
to be separated in two, I see it as one core. Similar to the fact
that NSString can also IO them without the need of an IO framework.
Cheers,
Alex
On 4-jul-2005, at 1:20, Koen van der Drift wrote:
>
> On Jul 3, 2005, at 3:12 PM, Philipp Seibel wrote:
>
>
>> Sorry, but i got lost :-). I just meant that we can't put all io
>> of all Frameworks in one IOFramework, because this IOFramework
>> will then depend on all Frameworks ( Foundation ,HMM,
>> Phylogenetics, etc.) because it will use the structure classes of
>> all of them. To solve this problem, we will need a seperate
>> IOFramework for each of the Frameworks.
>>
>>
>
> Aha, but now I understand :) I didn't realize that you were
> assuming different data structures for each data format. Maybe we
> should put some effort in creating a general internal data format
> that will also allow easy exchange between the various formats.
>
> cheers,
>
> - Koen.
>
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>
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** Alexander Griekspoor **
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